All Publications

  • ChatGPT Influence on Medical Decision-Making, Bias, and Equity: A Randomized Study of Clinicians Evaluating Clinical Vignettes. medRxiv : the preprint server for health sciences Goh, E., Bunning, B., Khoong, E., Gallo, R., Milstein, A., Centola, D., Chen, J. H. 2023


    In a randomized, pre-post intervention study, we evaluated the influence of a large language model (LLM) generative AI system on accuracy of physician decision-making and bias in healthcare. 50 US-licensed physicians reviewed a video clinical vignette, featuring actors representing different demographics (a White male or a Black female) with chest pain. Participants were asked to answer clinical questions around triage, risk, and treatment based on these vignettes, then asked to reconsider after receiving advice generated by ChatGPT+ (GPT4). The primary outcome was the accuracy of clinical decisions based on pre-established evidence-based guidelines. Results showed that physicians are willing to change their initial clinical impressions given AI assistance, and that this led to a significant improvement in clinical decision-making accuracy in a chest pain evaluation scenario without introducing or exacerbating existing race or gender biases. A survey of physician participants indicates that the majority expect LLM tools to play a significant role in clinical decision making.

    View details for DOI 10.1101/2023.11.24.23298844

    View details for PubMedID 38076944

    View details for PubMedCentralID PMC10705632

  • The evolving role of data & amp; safety monitoring boards for real-world clinical trials JOURNAL OF CLINICAL AND TRANSLATIONAL SCIENCE Bunning, B. J., Hedlin, H., Chen, J. H., Ciolino, J. D., Ferstad, J., Fox, E., Garcia, A., Go, A., Johari, R., Lee, J., Maahs, D. M., Mahaffey, K. W., Opsahl-Ong, K., Perez, M., Rochford, K., Scheinker, D., Spratt, H., Turakhia, M. P., Desai, M. 2023; 7 (1)
  • The evolving role of data & safety monitoring boards for real-world clinical trials. Journal of clinical and translational science Bunning, B. J., Hedlin, H., Chen, J. H., Ciolino, J. D., Ferstad, J. O., Fox, E., Garcia, A., Go, A., Johari, R., Lee, J., Maahs, D. M., Mahaffey, K. W., Opsahl-Ong, K., Perez, M., Rochford, K., Scheinker, D., Spratt, H., Turakhia, M. P., Desai, M. 2023; 7 (1): e179


    Clinical trials provide the "gold standard" evidence for advancing the practice of medicine, even as they evolve to integrate real-world data sources. Modern clinical trials are increasingly incorporating real-world data sources - data not intended for research and often collected in free-living contexts. We refer to trials that incorporate real-world data sources as real-world trials. Such trials may have the potential to enhance the generalizability of findings, facilitate pragmatic study designs, and evaluate real-world effectiveness. However, key differences in the design, conduct, and implementation of real-world vs traditional trials have ramifications in data management that can threaten their desired rigor.Three examples of real-world trials that leverage different types of data sources - wearables, medical devices, and electronic health records are described. Key insights applicable to all three trials in their relationship to Data and Safety Monitoring Boards (DSMBs) are derived.Insight and recommendations are given on four topic areas: A. Charge of the DSMB; B. Composition of the DSMB; C. Pre-launch Activities; and D. Post-launch Activities. We recommend stronger and additional focus on data integrity.Clinical trials can benefit from incorporating real-world data sources, potentially increasing the generalizability of findings and overall trial scale and efficiency. The data, however, present a level of informatic complexity that relies heavily on a robust data science infrastructure. The nature of monitoring the data and safety must evolve to adapt to new trial scenarios to protect the rigor of clinical trials.

    View details for DOI 10.1017/cts.2023.582

    View details for PubMedID 37745930

    View details for PubMedCentralID PMC10514684

  • Evaluation of acebilustat, a selective inhibitor of leukotriene B4 biosynthesis, for treatment of outpatients with mild-moderate COVID-19 disease: A randomized, double-blind, placebo- controlled Phase 2 trial. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Levitt, J. E., Hedlin, H., Duong, S., Lu, D., Lee, J., Bunning, B., Elkarra, N., Pinsky, B. A., Heffernan, E., Springman, E., Moss, R. B., Bonilla, H. F., Parsonnet, J., Zamanian, R. T., Langguth, J. J., Bollyky, J., Khosla, C., Nicolls, M. R., Desai, M., Rogers, A. J. 2023


    The vast majority of COVID-19 disease occurs in outpatients where treatment is limited to anti-virals for high-risk subgroups. Acebilustat, a leukotriene B4 (LTB4) inhibitor, has potential to reduce inflammation and symptom duration.In a single-center trial spanning Delta and Omicron variants, outpatients were randomized to 100 mg of oral acebilustat or placebo for 28 days. Patients reported daily symptoms via electronic query through Day 28 with phone follow-up on Day 120 and collected nasal swabs on Days 1-10. The primary outcome was sustained symptom resolution to Day 28. Secondary 28-day outcomes included time to first symptom resolution, area under the curve (AUC) of longitudinal daily symptom scores; duration of viral shedding through Day 10; and symptoms on Day 120.Sixty participants were randomized to each study arm. At enrollment, median duration and number of symptoms were 4 (IQR 3-5) days and 9 (IQR 7-11) symptoms. Most patients (90%) were vaccinated with 73% having neutralizing antibodies. A minority (44%) of participants (35% in the acebilustat arm and 53% in placebo) had sustained symptom resolution at Day 28 (HR 0.6, 95% CI 0.34-1.04, p = 0.07 favoring placebo). There was no difference in mean AUC of symptom scores over 28 days (difference in mean of AUC 9.4, 95% CI -42.1-60.9, p=0.72). Acebilustat did not impact viral shedding or symptoms at Day 120.Sustained symptoms through Day 28 were common in this low-risk population. Despite this, LTB4 antagonism with acebilustat did not shorten symptom duration in outpatients with COVID-19.

    View details for DOI 10.1093/cid/ciad187

    View details for PubMedID 36996150

  • Favipiravir for treatment of outpatients with asymptomatic or uncomplicated COVID-19: a double-blind randomized, placebo-controlled, phase 2 trial. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Holubar, M., Subramanian, A., Purington, N., Hedlin, H., Bunning, B., Walter, K. S., Bonilla, H., Boumis, A., Chen, M., Clinton, K., Dewhurst, L., Epstein, C., Jagannathan, P., Kaszynski, R. H., Panu, L., Parsonnet, J., Ponder, E. L., Quintero, O., Sefton, E., Singh, U., Soberanis, L., Truong, H., Andrews, J. R., Desai, M., Khosla, C., Maldonado, Y. 2022


    Favipiravir is an oral, RNA-dependent RNA polymerase inhibitor with in vitro activity against SARS-CoV2. Despite limited data, favipiravir is administered to patients with COVID-19 in several countries.We conducted a phase 2 double-blind randomized controlled outpatient trial of favipiravir in asymptomatic or mildly symptomatic adults with a positive SARS-CoV2 RT-PCR within 72 hours of enrollment. Participants were randomized 1: 1 to receive placebo or favipiravir (1800mg BID Day 1, 800 mg BID Days 2-10). The primary outcome was SARS-CoV-2 shedding cessation in a modified intention-to-treat (mITT) cohort of participants with positive enrollment RT-PCRs. Using SARS-CoV-2 amplicon-based sequencing, we assessed favipiravir's impact on mutagenesis.From July 8, 2020 - March 23, 2021, we randomized 149 participants with 116 included in the mITT cohort. The participants' mean age was 43 years (SD 12.5) and 57 (49%) were women. We found no difference in time to shedding cessation by treatment arm overall (HR 0.76 favoring placebo, 95% confidence interval [CI] 0.48-1.20) or in sub-group analyses (age, sex, high-risk comorbidities, seropositivity or symptom duration at enrollment). We observed no difference in time to symptom resolution (initial: HR 0.84, 95% CI 0.54-1.29; sustained: HR 0.87, 95% CI 0.52-1.45). We detected no difference in accumulation of transition mutations in the viral genome during treatment.Our data do not support favipiravir use at commonly used doses in outpatients with uncomplicated COVID-19. Further research is needed to ascertain if higher doses of favipiravir are effective and safe for patients with COVID-19.

    View details for DOI 10.1093/cid/ciac312

    View details for PubMedID 35446944

  • The COVID-19 Outpatient Pragmatic Platform Study (COPPS): Study design of a multi-center pragmatic platform trial. Contemporary clinical trials Bunning, B., Hedlin, H., Purington, N., Sundaram, V., Kapphahn, K., Weng, Y., Cunanan, K., Maldonado, Y., Singh, U., Khosla, C., O'Hara, R., Nicolls, M., Springman, E., Parsonnet, J., Rogers, A., Levitt, J., Desai, M. 2021: 106509


    More than 3000 clinical trials related to COVID-19 have been registered through With so many trials, there is a risk that many will be inconclusive due to being underpowered or due to an inability to recruit patients. At academic medical centers, multiple trials are competing for the same resources; the success of one may come at the expense of another. The COVID-19 Outpatient Pragmatic Protocol Study (COPPS) is a flexible phase 2, multi-site, randomized, blinded trial based at Stanford University designed to overcome these issues by simultaneously evaluating multiple COVID-19 treatments in the outpatient setting in one common platform with shared controls. This approach reduces the overall number of patients required for statistical power, while improving the likelihood that any enrolled patient receives active treatment. The platform study has two main domains designed to evaluate COVID-19 treatments by assessing their ability to reduce viral shedding (Viral Domain), measured with self-collected nasal swabs, or improve clinical outcomes (Clinical Domain), measured through self-reported symptomology data. Data are collected on both domains for all participants enrolled. Participants are followed over a 28-day period. COPPS has the advantage of pragmatism created around its workflow that is also appealing to potential participants because of a lower probability of inactive treatment. At the conclusion of this clinical trial we expect to have identified potentially effective therapeutic strategy/ies for treating COVID-19 in the outpatient setting, which will have a transformative impact on medicine and public health.

    View details for DOI 10.1016/j.cct.2021.106509

    View details for PubMedID 34274494

  • A positive feedback loop reinforces the allergic immune response in human peanut allergy. The Journal of experimental medicine Zhou, X., Yu, W., Lyu, S., Macaubas, C., Bunning, B., He, Z., Mellins, E. D., Nadeau, K. C. 2021; 218 (7)


    Food allergies are a leading cause of anaphylaxis, and cellular mechanisms involving antigen presentation likely play key roles in their pathogenesis. However, little is known about the response of specific antigen-presenting cell (APC) subsets to food allergens in the setting of food allergies. Here, we show that in peanut-allergic humans, peanut allergen drives the differentiation of CD209+ monocyte-derived dendritic cells (DCs) and CD23+ (FcєRII) myeloid dendritic cells through the action of allergen-specific CD4+ T cells. CD209+ DCs act reciprocally on the same peanut-specific CD4+ T cell population to reinforce Th2 cytokine expression in a positive feedback loop, which may explain the persistence of established food allergy. In support of this novel model, we show clinically that the initiation of oral immunotherapy (OIT) in peanut-allergic patients is associated with a decrease in CD209+ DCs, suggesting that breaking the cycle of positive feedback is associated with therapeutic effect.

    View details for DOI 10.1084/jem.20201793

    View details for PubMedID 33944900

  • Novel application of a discrete time-to-event model for randomized oral immunotherapy clinical trials with repeat food challenges. Statistics in medicine Purington, N., Andorf, S., Bunning, B., Chinthrajah, S., Nadeau, K., Desai, M. 2021


    The evaluation of double-blind, placebo-controlled food challenges (DBPCFC) generally focuses on a participant passing a challenge at a predetermined dose, and does not consider the dose of reaction for those who fail or are censored due to study discontinuation. Further, a number of food allergy trials have incorporated multiple DBPCFCs throughout the duration of the study in order to evaluate changes in reaction over time including sustained unresponsiveness from treatment. Outcomes arising from these trials are commonly modeled using Chi-squared or Fisher's exact tests at each time point. We propose applying time-to-event methodology to food allergy trials in order to exploit the inherent granularity of challenge outcomes that additionally accommodates repeated DBPCFCs. Specifically, we consider dose-to-failure for each study challenge and extend the cumulative tolerated dose across challenges to result in a dose-time axis. A discrete time-to-event framework is applied to the dose-time outcome to assess the efficacy of treatment across the entire study period. We illustrate ideas with data from the Peanut Oral Immunotherapy Study: Safety, Efficacy and Discovery (POISED) trial, conducted at Stanford University, which evaluated the efficacy of oral immunotherapy on desensitization and sustained unresponsiveness in peanut allergic children and adults. We demonstrate the advantages of time-to-event approaches for assessing the efficacy of treatment over time and incorporating information for those who failed or were lost to follow up. Further, we introduce a dose-time outcome that is interpretable to clinicians and allows for examination of such outcomes over time.

    View details for DOI 10.1002/sim.9019

    View details for PubMedID 33959986

  • Immune Changes Beyond Th2 Pathways During Rapid Multifood Immunotherapy enabled with Omalizumab. Allergy Manohar, M., Dunham, D., Gupta, S., Yan, Z., Zhang, W., Minnicozzi, S., Kirkey, M., Bunning, B., Chowdhury, R. R., Galli, S. J., Boyd, S. D., Kost, L. E., Chinthrajah, R. S., Desai, M., Oettgen, H. C., Maecker, H. T., Yu, W., DeKruyff, R. H., Andorf, S., Nadeau, K. C. 2021


    BACKGROUND: Multifood Oral Immunotherapy (mOIT) with adjunctive anti-IgE (omalizumab, Xolair ) treatment affords safe, effective, and rapid desensitization to multiple foods, although the specific immune mechanisms mediating this desensitization remain to be fully elucidated.METHODS: Participants in our phase 2 mOIT trial (NCT02643862) received omalizumab from baseline to week 16 and mOIT from week 8 to week 36. We compared the immune profile of PBMCs and plasma taken at baseline, week 8 and week 36 using high-dimensional mass cytometry, component-resolved diagnostics, the indirect basophil activation test, and Luminex.RESULTS: We found (i) decreased frequency of IL4+ peanut-reactive CD4+ T cells and a marked downregulation of GPR15 expression and CXCR3 frequency among gammadelta and CD8+ T cell subsets at week 8 during the initial, omalizumab-alone induction phase; (ii) significant upregulation of the skin-homing receptor CCR4 in peanut-reactive CD4+ T and Th2 effector memory (EM) cells and of cutaneous lymphocyte-associated antigen (CLA) in peanut-reactive CD8+ T and CD8+ EM cells (iii) downregulation of CD86 expression among antigen-presenting cell subsets; and (iv) reduction in pro-inflammatory cytokines, notably IL-17, at week 36 post-OIT. We also observed significant attenuation of the Th2 phenotype post-OIT, defined by downregulation of IL-4 peanut-reactive T cells and OX40 in Th2EM cells, increased allergen component-specific IgG4/IgE ratio, and decreased allergen-driven activation of indirectly sensitized basophils.CONCLUSIONS: This exploratory study provides novel comprehensive insight into the immune underpinnings of desensitization through omalizumab-facilitated mOIT. Moreover, this study provides encouraging results to support the complex immune changes that can be induced by OIT.

    View details for DOI 10.1111/all.14833

    View details for PubMedID 33782956

  • Clinical trials in a COVID-19 pandemic: Shared infrastructure for continuous learning in a rapidly changing landscape. Clinical trials (London, England) Hedlin, H. n., Garcia, A. n., Weng, Y. n., He, Z. n., Sundaram, V. n., Bunning, B. n., Balasubramanian, V. n., Cunanan, K. n., Kapphahn, K. n., Gummidipundi, S. n., Purington, N. n., Boulos, M. n., Desai, M. n. 2021: 1740774520988298


    Clinical trials, conducted efficiently and with the utmost integrity, are a key component in identifying effective vaccines, therapies, and other interventions urgently needed to solve the COVID-19 crisis. Yet launching and implementing trials with the rigor necessary to produce convincing results is a complicated and time-consuming process. Balancing rigor and efficiency involves relying on designs that employ flexible features to respond to a fast-changing landscape, measuring valid endpoints that result in translational actions and disseminating findings in a timely manner. We describe the challenges involved in creating infrastructure with potential utility for shared learning.We have established a shared infrastructure that borrows strength across multiple trials. The infrastructure includes an endpoint registry to aid in selecting appropriate endpoints, a registry to facilitate establishing a Data & Safety Monitoring Board, common data collection instruments, a COVID-19 dedicated design and analysis team, and a pragmatic platform protocol, among other elements.The authors have relied on the shared infrastructure for six clinical trials for which they serve as the Data Coordinating Center and have a design and analysis team comprising 15 members who are dedicated to COVID-19. The authors established a pragmatic platform to simultaneously investigate multiple treatments for the outpatient with adaptive features to add or drop treatment arms.The shared infrastructure provides appealing opportunities to evaluate disease in a more robust manner with fewer resources and is especially valued during a pandemic where efficiency in time and resources is crucial. The most important element of the shared infrastructure is the pragmatic platform. While it may be the most challenging of the elements to establish, it may provide the greatest benefit to both patients and researchers.

    View details for DOI 10.1177/1740774520988298

    View details for PubMedID 33535821

  • Targeted DNA methylation profiling reveals epigenetic signatures in peanut allergy. JCI insight Zhou, X. n., Han, X. n., Lyu, S. C., Bunning, B. J., Kost, L. n., Chang, I. n., Cao, S. n., Sampath, V. n., Nadeau, K. C. 2021


    DNA methylation (DNAm) has been shown to play a role in mediating food allergy, however, the mechanism by which it does so is poorly understood. In this study, we used targeted NextGen bisulfite sequencing to evaluate DNAm levels in 125 targeted highly informative genomic regions containing 602 CpG sites on 70 immune-related genes to understand whether DNAm can differentiate peanut allergy (PA) vs non-allergy (NA). We found PA-associated DNAm signatures associated with 12 genes (7 novel to food allergy, 3 associated with Th1/Th2, and 2 associated with innate immunity) as well as DNAm signature combinations with superior diagnostic potential compared to serum peanut specific-IgE for PA vs. NA. Further, we found that following peanut protein stimulation, peripheral blood mononuclear cell (PBMCs) from PA participants showed increased production of cognate cytokines compared to NA participants. The varying responses between PA and NA participants may be associated with the interaction between the modification of DNAm and the interference of environment. Using Euclidean distance analysis, we found that the distances of methylation profile comprising 12 DNAm signatures between PA and NA pairs in monozygotic (MZ) twins were smaller than that in randomly paired genetically unrelated individuals, suggesting that PA related DNAm signatures may be associated with genetic factors.

    View details for DOI 10.1172/jci.insight.143058

    View details for PubMedID 33571165

  • RNA-Seq of Gastrointestinal Biopsies During Oral Immunotherapy Reveals Changes in IgA Pathway Zhang, W., Dhondalay, G., Hoh, R., Tupa, D., Bunning, B., Fernandez-Becker, N., Kambham, N., Boyd, S., Galli, S., Andorf, S., Manohar, M., Chinthrajah, S., Nadeau, K. MOSBY-ELSEVIER. 2020: AB132
  • Peanut oral immunotherapy induces gastrointestinal eosinophilia in a longitudinal randomized controlled trial Wright, B., Fernandez-Becker, N., Kambham, N., Purington, N., Cao, S., Tupa, D., Zhang, W., Rank, M., Kita, H., Katzka, D., Shim, K., Bunning, B., Doyle, A., Jacobsen, E., Boyd, S., Manohar, M., Galli, S., Nadeau, K., Chinthrajah, S. MOSBY-ELSEVIER. 2020: AB84
  • Gastrointestinal Eosinophil Responses in a Longitudinal, Randomized Trial of Peanut Oral Immunotherapy. Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association Wright, B. L., Fernandez-Becker, N. Q., Kambham, N. n., Purington, N. n., Cao, S. n., Tupa, D. n., Zhang, W. n., Sindher, S. B., Rank, M. A., Kita, H. n., Katzka, D. A., Shim, K. P., Bunning, B. J., Doyle, A. D., Jacobsen, E. A., Tsai, M. n., Boyd, S. D., Manohar, M. n., Chinthrajah, R. S. 2020


    Gastrointestinal side effects are common during oral immunotherapy (OIT) and eosinophilic esophagitis (EoE) is a potential complication. We aimed to characterize eosinophilic gastrointestinal responses to peanut OIT, in which peanut protein is given orally, with incremental increases in dose over time.Twenty adults with IgE-mediated peanut allergy were randomly assigned to groups given peanut OIT (n=15) or placebo (n=5); 1 additional subject withdrew before randomization. Serial gastrointestinal biopsies were collected at baseline (n=21, 0 weeks), following dose escalation (n=10, 52 weeks), and during the maintenance phase (n=11, 104 weeks). Endoscopic findings were characterized using the EoE endoscopic reference score. Biopsies were assessed for eosinophils per high-power field (eos/hpf) and other pathology features using EoE histologic scoring system scores. We performed immunohistochemical analyses of eosinophil peroxidase deposition, quantified using automated image analysis.At baseline, no subjects reported current gastrointestinal symptoms. However, 3 of the 21 subjects (14%) had esophageal peak eosinophil counts ≥15 eos/hpf and all subjects had dilated intercellular spaces (DIS). OIT induced or exacerbated esophageal eosinophilia (EE) at 52 weeks in most subjects (peak eosinophil counts >5 eos/hpf in 6 of 7 patients [86%]; peak eosinophil counts ≥15 eos/hpf in 4 of 7 patients [57%]). One subject met clinicopathologic criteria for EoE and withdrew; no significant changes in esophageal peak eosinophil counts were observed in the placebo group. EE in the OIT group corresponded with significant increases in EoE histologic scoring system scores and deposition of eosinophil peroxidase. In 4 of 6 participants (67%), OIT-induced EE and gastrointestinal eosinophilia resolved by the end of the maintenance phase. Gastrointestinal symptoms were not clearly associated with EE or gastrointestinal eosinophilia.In this pilot study, we found that peanut OIT-induced EE and gastrointestinal eosinophilia are usually transient and are not always associated with gastrointestinal symptoms. no: NCT02103270.

    View details for DOI 10.1016/j.cgh.2020.05.019

    View details for PubMedID 32434067

  • Origins and clonal convergence of gastrointestinal IgE+ B cells in human peanut allergy. Science immunology Hoh, R. A., Joshi, S. A., Lee, J. Y., Martin, B. A., Varma, S. n., Kwok, S. n., Nielsen, S. C., Nejad, P. n., Haraguchi, E. n., Dixit, P. S., Shutthanandan, S. V., Roskin, K. M., Zhang, W. n., Tupa, D. n., Bunning, B. J., Manohar, M. n., Tibshirani, R. n., Fernandez-Becker, N. Q., Kambham, N. n., West, R. B., Hamilton, R. G., Tsai, M. n., Galli, S. J., Chinthrajah, R. S., Nadeau, K. C., Boyd, S. D. 2020; 5 (45)


    B cells in human food allergy have been studied predominantly in the blood. Little is known about IgE+ B cells or plasma cells in tissues exposed to dietary antigens. We characterized IgE+ clones in blood, stomach, duodenum, and esophagus of 19 peanut-allergic patients, using high-throughput DNA sequencing. IgE+ cells in allergic patients are enriched in stomach and duodenum, and have a plasma cell phenotype. Clonally related IgE+ and non-IgE-expressing cell frequencies in tissues suggest local isotype switching, including transitions between IgA and IgE isotypes. Highly similar antibody sequences specific for peanut allergen Ara h 2 are shared between patients, indicating that common immunoglobulin genetic rearrangements may contribute to pathogenesis. These data define the gastrointestinal tract as a reservoir of IgE+ B lineage cells in food allergy.

    View details for DOI 10.1126/sciimmunol.aay4209

    View details for PubMedID 32139586

  • Epigenetics and the Environment in Airway Disease: Asthma and Allergic Rhinitis. Advances in experimental medicine and biology Long, A., Bunning, B., Sampath, V., DeKruyff, R. H., Nadeau, K. C. 2020; 1253: 153–81


    Asthma and rhinitis are complex, heterogeneous diseases characterized by chronic inflammation of the upper and lower airways. While genome-wide association studies (GWAS) have identified a number of susceptible loci and candidate genes associated with the pathogenesis of asthma and allergic rhinitis (AR), the risk-associated alleles account for only a very small percent of the genetic risk. In allergic airway and other complex diseases, it is thought that epigenetic modifications, including DNA methylation, histone modifications, and non-coding microRNAs, caused by complex interactions between the underlying genome and the environment may account for some of this "missing heritability" and may explain the high degree of plasticity in immune responses. In this chapter, we will focus on the current knowledge of classical epigenetic modifications, DNA methylation and histone modifications, and their potential role in asthma and AR. In particular, we will review epigenetic variations associated with maternal airway disease, demographics, environment, and non-specific associations. The role of specific genetic haplotypes in environmentally induced epigenetic changes are also discussed. A major limitation of many of the current studies of asthma epigenetics is that they evaluate epigenetic modifications in both allergic and non-allergic asthma, making it difficult to distinguish those epigenetic modifications that mediate allergic asthma from those that mediate non-allergic asthma. Additionally, most DNA methylation studies in asthma use peripheral or cord blood due to poor accessibility of airway cells or tissue. Unlike DNA sequences, epigenetic alterations are quite cell- and tissue-specific, and epigenetic changes found in airway tissue or cells may be discordant from that of circulating blood. These two confounding factors should be considered when reviewing epigenetic studies in allergic airway disease.

    View details for DOI 10.1007/978-981-15-3449-2_6

    View details for PubMedID 32445095

  • The future of omics for clinical practice ANNALS OF ALLERGY ASTHMA & IMMUNOLOGY Long, A., Bunning, B., Borro, M., Sampath, V., Nadeau, K. C. 2019; 123 (6): 535–36

    View details for DOI 10.1016/j.anai.2019.07.016

    View details for Web of Science ID 000498692800004

    View details for PubMedID 31351978

  • Transcriptomic and methylomic features in asthmatic and non-asthmatic twins. Allergy Dhondalay, G. K., Bunning, B., Bauer, R. N., Barnathan, E. S., Maniscalco, C., Baribaud, F., Nadeau, K. C., Andorf, S. 2019

    View details for DOI 10.1111/all.14128

    View details for PubMedID 31758558

  • Trends in egg specific immunoglobulin levels during natural tolerance and oral immunotherapy. Allergy Andorf, S., Bunning, B., Tupa, D., Cao, S., Long, A. J., Borres, M. P., Galli, S. J., Chinthrajah, R. S., Nadeau, K. C. 2019

    View details for DOI 10.1111/all.14107

    View details for PubMedID 31724180

  • Effectiveness Of Clinician Dose Blinding In An Oral Immunotherapy Protocol Woch, M., O'Laughlin, K., Tan, T., Long, A. J., Bunning, B. J., Kumar, D., Chinthrajah, R., Nadeau, K. C. MOSBY-ELSEVIER. 2019: AB73
  • Multi-Omic Profiling Of Asthma Using High-Throughput Sequencing Dhondalay, G., Bunning, B. J., Nadeau, K. C., Andorf, S. MOSBY-ELSEVIER. 2019: AB203
  • Component IgE and IgG4 levels in patients with natural tolerance or oral immunotherapy treatment Bunning, B. J., Long, A. J., Chinthrajah, R., Nadeau, K. C., Andorf, S. MOSBY-ELSEVIER. 2019: AB246
  • Global metabolic profiling to model biological processes of aging in twins. Aging cell Bunning, B. J., Contrepois, K. n., Lee-McMullen, B. n., Dhondalay, G. K., Zhang, W. n., Tupa, D. n., Raeber, O. n., Desai, M. n., Nadeau, K. C., Snyder, M. P., Andorf, S. n. 2019: e13073


    Aging is intimately linked to system-wide metabolic changes that can be captured in blood. Understanding biological processes of aging in humans could help maintain a healthy aging trajectory and promote longevity. We performed untargeted plasma metabolomics quantifying 770 metabolites on a cross-sectional cohort of 268 healthy individuals including 125 twin pairs covering human lifespan (from 6 months to 82 years). Unsupervised clustering of metabolic profiles revealed 6 main aging trajectories throughout life that were associated with key metabolic pathways such as progestin steroids, xanthine metabolism, and long-chain fatty acids. A random forest (RF) model was successful to predict age in adult subjects (≥16 years) using 52 metabolites (R2  = .97). Another RF model selected 54 metabolites to classify pediatric and adult participants (out-of-bag error = 8.58%). These RF models in combination with correlation network analysis were used to explore biological processes of healthy aging. The models highlighted established metabolites, like steroids, amino acids, and free fatty acids as well as novel metabolites and pathways. Finally, we show that metabolic profiles of twins become more dissimilar with age which provides insights into nongenetic age-related variability in metabolic profiles in response to environmental exposure.

    View details for DOI 10.1111/acel.13073

    View details for PubMedID 31746094

  • Baseline Gastrointestinal Eosinophilia Is Common in Oral Immunotherapy Subjects With IgE-Mediated Peanut Allergy FRONTIERS IN IMMUNOLOGY Wright, B. L., Fernandez-Becker, N. Q., Kambham, N., Purington, N., Tupa, D., Zhang, W., Rank, M. A., Kita, H., Shim, K. P., Bunning, B. J., Doyle, A. D., Jacobsen, E. A., Boyd, S. D., Tsai, M., Maecker, H., Manohar, M., Galli, S. J., Nadeau, K. C., Chinthrajah, R. 2018; 9
  • Baseline Gastrointestinal Eosinophilia Is Common in Oral Immunotherapy Subjects With IgE-Mediated Peanut Allergy. Frontiers in immunology Wright, B. L., Fernandez-Becker, N. Q., Kambham, N., Purington, N., Tupa, D., Zhang, W., Rank, M. A., Kita, H., Shim, K. P., Bunning, B. J., Doyle, A. D., Jacobsen, E. A., Boyd, S. D., Tsai, M., Maecker, H., Manohar, M., Galli, S. J., Nadeau, K. C., Chinthrajah, R. S. 2018; 9: 2624


    Rationale: Oral immunotherapy (OIT) is an emerging treatment for food allergy. While desensitization is achieved in most subjects, many experience gastrointestinal symptoms and few develop eosinophilic gastrointestinal disease. It is unclear whether these subjects have subclinical gastrointestinal eosinophilia (GE) at baseline. We aimed to evaluate the presence of GE in subjects with food allergy before peanut OIT. Methods: We performed baseline esophagogastroduodenoscopies on 21 adults before undergoing peanut OIT. Subjects completed a detailed gastrointestinal symptom questionnaire. Endoscopic findings were assessed using the Eosinophilic Esophagitis (EoE) Endoscopic Reference Score (EREFS) and biopsies were obtained from the esophagus, gastric antrum, and duodenum. Esophageal biopsies were evaluated using the EoE Histologic Scoring System. Immunohistochemical staining for eosinophil peroxidase (EPX) was also performed. Hematoxylin and eosin and EPX stains of each biopsy were assessed for eosinophil density and EPX/mm2 was quantified using automated image analysis. Results: All subjects were asymptomatic. Pre-existing esophageal eosinophilia (>5 eosinophils per high-power field [eos/hpf]) was present in five participants (24%), three (14%) of whom had >15 eos/hpf associated with mild endoscopic findings (edema, linear furrowing, or rings; median EREFS = 0, IQR 0-0.25). Some subjects also demonstrated basal cell hyperplasia, dilated intercellular spaces, and lamina propria fibrosis. Increased eosinophils were noted in the gastric antrum (>12 eos/hpf) or duodenum (>26 eos/hpf) in 9 subjects (43%). EPX/mm2 correlated strongly with eosinophil counts (r = 0.71, p < 0.0001). Conclusions: Pre-existing GE is common in adults with IgE-mediated peanut allergy. Eosinophilic inflammation (EI) in these subjects may be accompanied by mild endoscopic and histologic findings. Longitudinal data collection during OIT is ongoing.

    View details for DOI 10.3389/fimmu.2018.02624

    View details for PubMedID 30524424

    View details for PubMedCentralID PMC6261984

  • Epigenetic Changes During Food-Specific Immunotherapy. Current allergy and asthma reports Bunning, B. J., DeKruyff, R. H., Nadeau, K. C. 2016; 16 (12): 87-?


    The prevalence and severity of IgE-mediated food allergy has increased dramatically over the last 15 years and is becoming a global health problem. Multiple lines of evidence suggest that epigenetic modifications of the genome resulting from gene-environment interactions have a key role in the increased prevalence of atopic disease. In this review, we describe the recent evidence suggesting how epigenetic changes mediate susceptibility to food allergies, and discuss how immunotherapy (IT) may reverse these effects. We discuss the areas of the epigenome as yet unexplored in terms of food allergy and IT such as histone modification and chromatin accessibility, and new techniques that may be utilized in future studies.Recent findings provide strong evidence that DNA methylation of certain promoter regions such as Forkhead box protein 3 is associated with clinical reactivity, and further, can be changed during IT treatment. Reports on other epigenetic changes are limited but also show evidence of significant change based on both disease status and treatment. In comparison to epigenetic studies focusing on asthma and allergic rhinitis, food allergy remains understudied. However, within the next decade, it is likely that epigenetic modifications may be used as biomarkers to aid in diagnosis and treatment of food-allergic patients. DNA methylation at specific loci has shown associations between food challenge outcomes, successful desensitization treatment, and overall phenotype compared to healthy controls.

    View details for PubMedID 27943047